scPDB - 3gnv entry

Protein Data Bank Entry:

PDB ID : 3gnv

Resolution :2.750 Å

Experimental Method : X-ray

Deposition Date : 2009-03-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Genome polyprotein
ID:	POLG_HCVJ4
AC:	O92972
Organism:	Hepatitis C virus genotype 1b
Reign:	Viruses
TaxID:	420174
EC Number:	2.7.7.48

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	19.138
Number of residues:	39
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.171	1073.250

% Hydrophobic	% Polar
38.99	61.01
According to VolSite

Ligand :

HET Code:	XNZ
Formula:	C30H29ClN2O4
Molecular weight:	517.015 g/mol
DrugBank ID:	-
Buried Surface Area:	60.43 %
Polar Surface area:	78.87 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
28.1752	46.3424	98.5536

Binding mode :

What is Poseview ?

2D View
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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
CL37	CE1	PHE- 193	3.39	0	Hydrophobic	false
C27	CB	PRO- 197	3.49	0	Hydrophobic	false
C25	CD	ARG- 200	3.6	0	Hydrophobic	false
C23	CB	CYS- 366	4.02	0	Hydrophobic	false
C2	CB	CYS- 366	3.4	0	Hydrophobic	false
C1	CB	CYS- 366	3.71	0	Hydrophobic	false
C19	CB	CYS- 366	3.29	0	Hydrophobic	false
C6	CB	SER- 367	4.36	0	Hydrophobic	false
C23	CB	SER- 368	3.91	0	Hydrophobic	false
C29	CB	SER- 368	4.16	0	Hydrophobic	false
C29	CD1	LEU- 384	3.49	0	Hydrophobic	false
C28	CB	MET- 414	4.42	0	Hydrophobic	false
C21	CE	MET- 414	4.41	0	Hydrophobic	false
C35	CG	MET- 414	3.72	0	Hydrophobic	false
C26	CE	MET- 414	3.39	0	Hydrophobic	false
C35	CE2	TYR- 415	3.87	0	Hydrophobic	false
CL37	CD1	TYR- 448	3.53	0	Hydrophobic	false
O36	N	TYR- 448	3.05	144.42	H-Bond (Protein Donor)	false
O33	O	HOH- 660	2.87	123.63	H-Bond (Protein Donor)	false